Yes, Hegemony can be neutralized. I generally do not do that if I want to save core worlds because I definitely need to babysit the survivors in Hegemony systems from pirates, plus some money lost from decivilizing those worlds. However, I will steal their nanoforges so their expeditions are weaker and make it easier for my patrols to defend my systems.
If I really want Hegemony military colonies dead, I have no problem sat bombing them to get the job done now. Also, if I am willing to decivilize one world, I do not want to stop until all core worlds are dead and my faction is the last one standing with no one to oppose it except maybe the zombie pirates.